rs5755495
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000668433.1(LINC02885):n.14G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,872 control chromosomes in the GnomAD database, including 29,311 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.61 ( 29309 hom., cov: 31)
Exomes 𝑓: 0.55 ( 2 hom. )
Consequence
LINC02885
ENST00000668433.1 non_coding_transcript_exon
ENST00000668433.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.29
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC02885 | ENST00000668433.1 | n.14G>C | non_coding_transcript_exon_variant | 1/4 |
Frequencies
GnomAD3 genomes ? AF: 0.615 AC: 93241AN: 151730Hom.: 29274 Cov.: 31
GnomAD3 genomes
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GnomAD4 exome AF: 0.545 AC: 12AN: 22Hom.: 2 Cov.: 0 AF XY: 0.550 AC XY: 11AN XY: 20
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GnomAD4 genome ? AF: 0.615 AC: 93335AN: 151850Hom.: 29309 Cov.: 31 AF XY: 0.619 AC XY: 45918AN XY: 74204
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at